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- EMDB-48358: Pol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome DSIF loc... -

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Basic information

Entry
Database: EMDB / ID: EMD-48358
TitlePol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome DSIF local map E
Map dataPol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome DSIF local map E
Sample
  • Complex: RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome complex
    • Complex: DSIF (SPT4 and SPT5)
    • Complex: PAF1 complex (CTR9, CDC73, PAF1, LEO1, WDR61, RTF1)
      • Complex: PAF1 complex (CTR9, CDC73, PAF1, LEO1, WDR61)
      • Organelle or cellular component: RTF1
    • Complex: RNA polymerase II
    • Complex: Nucleosome
    • Organelle or cellular component: SPT6
    • Organelle or cellular component: TFIIS
    • Organelle or cellular component: IWS1
    • Organelle or cellular component: LEDGF
    • Organelle or cellular component: ELOF1
Keywordspolymerase / elongation factor / nucleosome / TRANSCRIPTION
Biological speciesHomo sapiens (human) / Sus scrofa (pig) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSyau D / Farnung L
Funding support United States, 3 items
OrganizationGrant numberCountry
Richard and Susan Smith Family Foundation United States
Damon Runyon Cancer Research Foundation United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)DP2-ES036404 United States
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Structure and function of IWS1 in transcription elongation.
Authors: Della Syau / Felix Steinruecke / Sophie Roth / Ernst Schmid / Karen Adelman / Johannes C Walter / Lucas Farnung /
Abstract: Transcription elongation by RNA polymerase II is a tightly regulated process that requires coordinated interactions between transcription elongation factors. IWS1 (Interacts with SPT6) has been ...Transcription elongation by RNA polymerase II is a tightly regulated process that requires coordinated interactions between transcription elongation factors. IWS1 (Interacts with SPT6) has been implicated as a core elongation factor, but its molecular role remains unclear. We show that the intrinsically disordered C-terminal region of IWS1 contains short linear motifs (SLiMs) that multivalently engage the elongation machinery. Using cryo-electron microscopy, we map SLiMs in IWS1 that interact with Pol II subunits RPB1, RPB2, and RPB5, as well as elongation factors DSIF, SPT6, and ELOF1. Functional assays demonstrate that distinct IWS1 SLiMs specify IWS1 recruitment and IWS1-dependent transcription stimulation. IWS1 recruitment to the transcription elongation complex depends on association via the RPB1 jaw and binding of downstream DNA. Transcription elongation stimulation requires interactions with the RPB2 lobe and ELOF1. We identify other transcription elongation factors including ELOA and RECQL5 that bind the RPB1 jaw and demonstrate that IWS1 protects the activated transcription elongation complex from RECQL5 inhibition. We also reveal the binding of the histone reader and IWS1 interactor LEDGF to a transcribed downstream nucleosome. Our findings establish IWS1 as a modular scaffold that helps organize the transcription elongation complex, illustrating how disordered regions regulate transcription elongation.
History
DepositionDec 19, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48358.png

Downloads & links

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Map

FileDownload / File: emd_48358.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome DSIF local map E
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 460 pix.
= 547.4 Å		1.19 Å/pix.
x 460 pix.
= 547.4 Å		1.19 Å/pix.
x 460 pix.
= 547.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.19 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.17272508 - 0.37598392
Average (Standard dev.)-0.0002584637 (±0.0066038943)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 547.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Pol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome DSIF local map E half map...

Fileemd_48358_half_map_1.map
AnnotationPol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome DSIF local map E half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Pol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome DSIF local map E half map...

Fileemd_48358_half_map_2.map
AnnotationPol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome DSIF local map E half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleoso...

EntireName: RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome complex
Components
  • Complex: RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome complex
    • Complex: DSIF (SPT4 and SPT5)
    • Complex: PAF1 complex (CTR9, CDC73, PAF1, LEO1, WDR61, RTF1)
      • Complex: PAF1 complex (CTR9, CDC73, PAF1, LEO1, WDR61)
      • Organelle or cellular component: RTF1
    • Complex: RNA polymerase II
    • Complex: Nucleosome
    • Organelle or cellular component: SPT6
    • Organelle or cellular component: TFIIS
    • Organelle or cellular component: IWS1
    • Organelle or cellular component: LEDGF
    • Organelle or cellular component: ELOF1

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Supramolecule #1: RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleoso...

SupramoleculeName: RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#32
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.7 MDa

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Supramolecule #3: DSIF (SPT4 and SPT5)

SupramoleculeName: DSIF (SPT4 and SPT5) / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: PAF1 complex (CTR9, CDC73, PAF1, LEO1, WDR61, RTF1)

SupramoleculeName: PAF1 complex (CTR9, CDC73, PAF1, LEO1, WDR61, RTF1) / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: PAF1 complex (CTR9, CDC73, PAF1, LEO1, WDR61)

SupramoleculeName: PAF1 complex (CTR9, CDC73, PAF1, LEO1, WDR61) / type: complex / ID: 5 / Parent: 4
Details: CTR9, CDC73, PAF1, LEO1, WDR61 expressed and purified together
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #10: RNA polymerase II

SupramoleculeName: RNA polymerase II / type: complex / ID: 10 / Parent: 1
Source (natural)Organism: Sus scrofa (pig)

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Supramolecule #12: Nucleosome

SupramoleculeName: Nucleosome / type: complex / ID: 12 / Parent: 1
Details: Nucleosome containing H3K36cme3-modified histone octamer and synthetic DNA
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #2: SPT6

SupramoleculeName: SPT6 / type: organelle_or_cellular_component / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #6: RTF1

SupramoleculeName: RTF1 / type: organelle_or_cellular_component / ID: 6 / Parent: 4 / Details: RTF1 expressed and purified separately
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #7: TFIIS

SupramoleculeName: TFIIS / type: organelle_or_cellular_component / ID: 7 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #8: IWS1

SupramoleculeName: IWS1 / type: organelle_or_cellular_component / ID: 8 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #9: LEDGF

SupramoleculeName: LEDGF / type: organelle_or_cellular_component / ID: 9 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #11: ELOF1

SupramoleculeName: ELOF1 / type: organelle_or_cellular_component / ID: 11 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
50.0 mMNaClsodium chloride
3.0 mMMgCl2magnesium chloride
1.0 mMTCEP(tris(2-carboxyethyl)phosphine)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: TFS Selectris
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 2 / Number real images: 30316 / Average exposure time: 4.21 sec. / Average electron dose: 37.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4597368
CTF correctionSoftware - Name: cryoSPARC (ver. 3.2.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 79487
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
FSC plot (resolution estimation)

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